Selecting connected pixels in a binary mask in 3D

Hi all,

I was wondering if anyone knew a way of selecting connected pixels in a binary mask in 3D to allow individual ‘objects’ within a image stack/volume to be selected? So similar to the wand tracing tool in 2D.

At the moment I do have a method of doing this but is quite convoluted: 3DObjectCounter > MapsToShowObject, then colour threshold to isolate my object of interest. This does work but I was wondering if there was another way…


Dear @Jonny251990,

Could you be more specific about what you are trying to achieve? In any case, selections/ROIs in ImageJ are restricted to one slice/plane as far as I know. However, it sounds like you are looking to generate a binary image from your selection?



Maybe you want to have a look to 3DManager :
you can select and manipulate individual objects from a segmented image (that is binary then labelled).



To add two more options to the discussion, you can do that in MorphoLibJ using two consecutive menu commands (as suggested by @ThomasBoudier):

  1. Plugins > MorphoLibJ > Binary Images > Connected Components Labeling to assign a different integer value to each 3D connected region.
  2. Plugins > MorphoLibJ > Label Images > Select Label(s) to create a new image with only the regions whose label number you select.

Or interactively by using Plugins > MorphoLibJ > Interactive Morphological Reconstruction 3D and reconstructing by dilation from the seed point you select: